recipe bioconductor-cernanetsim

Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ceRNAnetsim.html

License:

GPL (>= 3.0)

Recipe:

/bioconductor-cernanetsim/meta.yaml

This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.

package bioconductor-cernanetsim

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.1-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-furrr:

depends r-future:

depends r-ggplot2:

depends r-ggraph:

depends r-igraph:

depends r-purrr:

depends r-rlang:

depends r-tibble:

depends r-tidygraph:

depends r-tidyr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-cernanetsim

and update with::

   mamba update bioconductor-cernanetsim

To create a new environment, run:

mamba create --name myenvname bioconductor-cernanetsim

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-cernanetsim:<tag>

(see `bioconductor-cernanetsim/tags`_ for valid values for ``<tag>``)

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